Summary: Primary sclerosing cholangitis (PSC) is the main predisposing condition for the development of biliary tract cancers, including cholangiocarcinoma (CCA) and gallbladder cancer (GBC). These malignancies are rare and often detected at an advanced stage, resulting in extremely poor survival rates. To date, there are no effective tools for the early diagnosis, prognosis, or follow-up of CCA and GBC in patients with PSC. The biological mechanisms driving both PSC and biliary tract cancers remain largely unclear, which limits therapeutic progress. Since epigenetic regulation, and particularly DNA methylation, has emerged as a key hallmark of cancer and a dynamic process throughout life, we hypothesize that methylation alterations associated with these diseases can be detected in peripheral blood. The aim of this project is to identify such disease-related methylation changes that could (1) provide prognostic information on the evolution of PSC and (2) enable the early detection of CCA and GBC. The study also seeks to define disease-specific methylation signatures in order to improve biological understanding of these pathologies. Methods: DNA was isolated from whole blood samples of 110 individuals, including 40 patients with cholangiocarcinoma, 21 with gallbladder cancer, 29 with PSC with or without CCA, and 20 healthy controls. Genome-wide DNA methylation profiling was carried out using the Illumina Infinium EPIC BeadChip array, which covers approximately 850,000 CpG sites. The analyses were performed at the Bioinformatics and Expression Analysis (BEA) core facility at Karolinska Institutet, Campus Flemingsberg. Detailed clinical data were collected for all subjects, including patient outcomes such as overall survival for cancer patients, and transplantation, cancer occurrence, or death for PSC cases. The follow-up period extended beyond three years after surgery for CCA and GBC patients and up to thirteen years after blood collection for PSC patients. Expected results and perspectives : This project aims to generate the first comprehensive genome-wide DNA methylation profiles of biliary tract cancers and PSC. We expect to identify numerous differentially methylated sites and regions that distinguish CCA, GBC, and PSC from healthy individuals. Using machine learning approaches, we plan to discover combinations of methylation markers with strong diagnostic potential for the early detection of CCA and GBC. By integrating clinical follow-up data, we aim to identify specific methylation signatures capable of predicting disease outcomes, such as post-surgical survival and progression in PSC. Functional enrichment analysis will be performed to reveal genes and biological pathways involved in these disorders, potentially highlighting novel mechanisms of carcinogenesis and offering new biomarkers for prognosis and disease monitoring. In the long term, these findings could contribute to the development of a minimally invasive blood test for clinical use in PSC and biliary tract cancer management.